It's been 5 days and I am trying to find the translational potential of certain circRNAs, but since CircRNADb is not working anymore and without any proper paper mentioning that the circRNA has protein coding potential, I am currently stuck.
I tried searching for papers mentioning that ORF from CircBank can have protein coding potential, but still got none. What is the solution to this problem?
Raghad Mouhamad
ORF Analysis: Use tools like TransDecoder, ORF Finder (NCBI), or ExPASy to predict potential open reading frames (ORFs) in your circRNA sequences. You can also check for ribosome-associated RNA-seq data (Ribo-seq) to see if the circRNA is being translated. In Silico Tools: Use coding potential prediction tools like CPC2, CPAT, or CINCH to assess whether your circRNA has coding potential based on its sequence characteristics. Experimental Validation: You can experimentally validate translation by:Using luciferase reporter assays to check for translation. Performing Western blotting if you suspect a protein is being encoded. Mass spectrometry for detecting novel proteins associated with the circRNA. Explore New Databases: In addition to CircBank, check other resources like circAtlas or ciRPath for updated information on circRNA translation. Ribosome Association: To determine if a circRNA is translated, you can use techniques like ribosome immunoprecipitation (RIP) or polysome profiling. Experimental Strategies: If databases and predictions are insufficient, performing experimental validation in cell lines or tissues might be necessary.
To determine the translational potential of circRNAs, you can follow these approaches:
If CircRNADb is down, explore alternative databases for available data, such as circAtlas.
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